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1OKE
Asym. Unit
Info
Asym.Unit (140 KB)
Biol.Unit 1 (133 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE PROTEIN IN COMPLEX WITH N-OCTYL-BETA-D-GLUCOSIDE
Authors
:
Y. Modis, S. C. Harrison
Date
:
22 Jul 03 (Deposition) - 24 Jul 03 (Release) - 18 Jan 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Viral Protein, Membrane Fusion, Flavivirus, Fusion Peptide, Viral Protein, Low-Ph Conformational Change, Class 2 Fusion Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Modis, S. Ogata, D. Clements, S. C. Harrison
A Ligand-Binding Pocket In The Dengue Virus Envelope Glycoprotein.
Proc. Natl. Acad. Sci. Usa V. 100 6986 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 12)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: B-OCTYLGLUCOSIDE (BOGa)
2b: B-OCTYLGLUCOSIDE (BOGb)
3a: BETA-L-FUCOSE (FULa)
3b: BETA-L-FUCOSE (FULb)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
BOG
2
Ligand/Ion
B-OCTYLGLUCOSIDE
3
FUL
2
Ligand/Ion
BETA-L-FUCOSE
4
NAG
6
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:49 , ILE A:270 , GLN A:271 , LEU A:277
BINDING SITE FOR RESIDUE BOG A1400
2
AC2
SOFTWARE
THR B:48 , GLU B:49 , ALA B:50 , PHE B:193 , LEU B:207 , ILE B:270 , GLN B:271
BINDING SITE FOR RESIDUE BOG B1400
3
AC3
SOFTWARE
ASN A:67 , HOH A:2049
BINDING SITE FOR MONO-SACCHARIDE NAG A1395 BOUND TO ASN A 67
4
AC4
SOFTWARE
GLU A:147 , HIS A:149 , ASN A:153 , LYS A:157 , HIS A:158
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 153 RESIDUES 1396 TO 1399
5
AC5
SOFTWARE
ASN B:67 , HOH B:2084 , HOH B:2085 , HOH B:2086
BINDING SITE FOR MONO-SACCHARIDE NAG B1395 BOUND TO ASN B 67
6
AC6
SOFTWARE
GLU B:147 , HIS B:149 , ASN B:153 , LYS B:157 , HIS B:158 , HOH B:2087
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 153 RESIDUES 1396 TO 1399
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1okea1 (A:298-394)
1b: SCOP_d1okeb1 (B:298-394)
2a: SCOP_d1okea2 (A:1-297)
2b: SCOP_d1okeb2 (B:1-297)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
E set domains
(509)
Family
:
Class II viral fusion proteins C-terminal domain
(27)
Protein domain
:
Envelope glycoprotein
(14)
Dengue virus type 2 [TaxId: 11060]
(9)
1a
d1okea1
A:298-394
1b
d1okeb1
B:298-394
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Viral glycoprotein, central and dimerisation domains
(24)
Superfamily
:
Viral glycoprotein, central and dimerisation domains
(24)
Family
:
Viral glycoprotein, central and dimerisation domains
(17)
Protein domain
:
Envelope glycoprotein
(9)
Dengue virus type 2 [TaxId: 11060]
(7)
2a
d1okea2
A:1-297
2b
d1okeb2
B:1-297
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1okeA02 (A:52-63,A:122-130,A:191-232,A:253-267)
1b: CATH_1okeB02 (B:52-63,B:122-130,B:191-231,B:253-267)
2a: CATH_1okeB03 (B:64-121,B:232-252)
2b: CATH_1okeA03 (A:64-121,A:233-252)
3a: CATH_1okeA04 (A:295-394)
3b: CATH_1okeB04 (B:295-394)
4a: CATH_1okeB01 (B:1-51,B:131-190,B:269-294)
4b: CATH_1okeA01 (A:1-51,A:131-190,A:268-294)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Viral Envelope Glycoprotein; domain 2
(12)
Homologous Superfamily
:
Viral Envelope Glycoprotein, domain 2
(12)
Dengue virus type 2. Organism_taxid: 11060. Strain: pr159/s1.
(2)
1a
1okeA02
A:52-63,A:122-130,A:191-232,A:253-267
1b
1okeB02
B:52-63,B:122-130,B:191-231,B:253-267
Topology
:
Viral Envelope Glycoprotein; domain 3
(12)
Homologous Superfamily
:
Viral Envelope Glycoprotein, domain 3
(12)
Dengue virus type 2. Organism_taxid: 11060. Strain: pr159/s1.
(2)
2a
1okeB03
B:64-121,B:232-252
2b
1okeA03
A:64-121,A:233-252
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.350, no name defined]
(26)
Dengue virus type 2. Organism_taxid: 11060. Strain: pr159/s1.
(2)
3a
1okeA04
A:295-394
3b
1okeB04
B:295-394
Topology
:
Tick-borne Encephalitis virus Glycoprotein; domain 1
(14)
Homologous Superfamily
:
Tick-borne Encephalitis virus Glycoprotein, domain 1
(14)
Dengue virus type 2. Organism_taxid: 11060. Strain: pr159/s1.
(2)
4a
1okeB01
B:1-51,B:131-190,B:269-294
4b
1okeA01
A:1-51,A:131-190,A:268-294
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Flavi_glycop_C_1okeB01 (B:298-393)
1b: PFAM_Flavi_glycop_C_1okeB02 (B:298-393)
2a: PFAM_Flavi_glycoprot_1okeB03 (B:1-296)
2b: PFAM_Flavi_glycoprot_1okeB04 (B:1-296)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Flavi_glycop_C]
(15)
Family
:
Flavi_glycop_C
(15)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(2)
1a
Flavi_glycop_C-1okeB01
B:298-393
1b
Flavi_glycop_C-1okeB02
B:298-393
Clan
:
no clan defined [family: Flavi_glycoprot]
(10)
Family
:
Flavi_glycoprot
(10)
Dengue virus type 2 (strain Puerto Rico/PR159-S1/1969) (DENV-2)
(2)
2a
Flavi_glycoprot-1okeB03
B:1-296
2b
Flavi_glycoprot-1okeB04
B:1-296
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Asymmetric Unit 1
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